Refactor Filter class (#32)

* Filter -> FilterResult * do not update collate field * add assert_filter_result * more Filter -> FilterResult * return a data.table for .$calculate() * add a test for .$combine() * do not export assert fun * minor * tetsts and more Filter -> FilterResult * also export feature names * - use mlr3pipelines way to register filter - add printer - restructure dictionary * update tests * doc * remove dup * doc * import backports * silence R CMD check warning * update examples * upd tic, solve pkgdown errors * style and fix readme * fix test * fix superclass
mlr-org · Jun 19, 2019 · d8fefd9 · d8fefd9
1 parent da35a75
commit d8fefd9
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diff --git a/.travis.yml b/.travis.yml
@@ -34,5 +34,4 @@ env:
   global:
   - _R_CHECK_FORCE_SUGGESTS_=false
   - MAKEFLAGS="-j 2"
-  - BUILD_PKGDOWN=true
   - _R_CHECK_TESTS_NLINES_=0
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -25,6 +25,7 @@ BugReports: https://github.com/mlr-org/mlr3featsel/issues
 Depends:
     R (>= 3.1.0)
 Imports:
+    backports,
     checkmate,
     data.table,
     mlr3,
@@ -57,7 +58,8 @@ NeedsCompilation: no
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 6.1.1
 Collate:
-    'Filter.R'
+    'mlr_filters.R'
+    'FilterResult.R'
     'FilterAUC.R'
     'FilterCMIM.R'
     'FilterDISR.R'
@@ -74,7 +76,7 @@ Collate:
     'FilterSymmetricalUncertainty.R'
     'FilterVariableImportance.R'
     'FilterVariance.R'
+    'helper_expectations.R'
     'helpers.R'
-    'mlr_filters.R'
     'reexports.R'
     'zzz.R'
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,8 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(as.data.table,DictionaryFilter)
-S3method(as.data.table,Filter)
-export(Filter)
+S3method(as.data.table,DictionaryFilterResult)
+S3method(as.data.table,FilterResult)
 export(FilterAUC)
 export(FilterCMIM)
 export(FilterDISR)
@@ -16,6 +15,7 @@ export(FilterMIM)
 export(FilterMRMR)
 export(FilterNJMIM)
 export(FilterRankCorrelation)
+export(FilterResult)
 export(FilterSymmetricalUncertainty)
 export(FilterVariableImportance)
 export(FilterVariance)

diff --git a/R/FilterAUC.R b/R/FilterAUC.R
@@ -1,7 +1,7 @@
 #' @title AUC Filter
 #'
 #' @aliases mlr_filters_auc
-#' @format [R6::R6Class] inheriting from [Filter].
+#' @format [R6::R6Class] inheriting from [FilterResult].
 #' @include Filter.R
 #'
 #' @description
@@ -14,8 +14,8 @@
 #' task = mlr3::mlr_tasks$get("sonar")
 #' filter = FilterAUC$new()
 #' filter$calculate(task)
-#' head(as.data.table(filter), 3)
-FilterAUC = R6Class("FilterAUC", inherit = Filter,
+#' as.data.table(filter)[1:3]
+FilterAUC = R6Class("FilterAUC", inherit = FilterResult,
   public = list(
     initialize = function(id = "auc") {
       super$initialize(
@@ -37,3 +37,5 @@ FilterAUC = R6Class("FilterAUC", inherit = Filter,
     }
   )
 )
+
+register_filter("auc", FilterAUC)
diff --git a/R/FilterCMIM.R b/R/FilterCMIM.R
@@ -1,7 +1,7 @@
 #' @title Minimal Conditional Mutual Information Filter
 #'
 #' @aliases mlr_filters_cmim
-#' @format [R6::R6Class] inheriting from [Filter].
+#' @format [R6::R6Class] inheriting from [FilterResult].
 #' @include Filter.R
 #'
 #' @description
@@ -14,8 +14,8 @@
 #' task = mlr3::mlr_tasks$get("iris")
 #' filter = FilterCMIM$new()
 #' filter$calculate(task)
-#' head(as.data.table(filter), 3)
-FilterCMIM = R6Class("FilterCMIM", inherit = Filter,
+#' as.data.table(filter)[1:3]
+FilterCMIM = R6Class("FilterCMIM", inherit = FilterResult,
   public = list(
     initialize = function(id = "cmim") {
       super$initialize(
@@ -35,3 +35,5 @@ FilterCMIM = R6Class("FilterCMIM", inherit = Filter,
     }
   )
 )
+
+register_filter("cmim", FilterCMIM)
diff --git a/R/FilterDISR.R b/R/FilterDISR.R
@@ -1,7 +1,7 @@
 #' @title Double Input Symmetrical Relevance Filter
 #'
 #' @aliases mlr_filters_disr
-#' @format [R6::R6Class] inheriting from [Filter].
+#' @format [R6::R6Class] inheriting from [FilterResult].
 #' @include Filter.R
 #'
 #' @description
@@ -14,8 +14,8 @@
 #' task = mlr3::mlr_tasks$get("iris")
 #' filter = FilterDISR$new()
 #' filter$calculate(task)
-#' head(as.data.table(filter), 3)
-FilterDISR = R6Class("FilterDISR", inherit = Filter,
+#' as.data.table(filter)[1:3]
+FilterDISR = R6Class("FilterDISR", inherit = FilterResult,
   public = list(
     initialize = function(id = "disr") {
       super$initialize(
@@ -35,3 +35,5 @@ FilterDISR = R6Class("FilterDISR", inherit = Filter,
     }
   )
 )
+
+register_filter("disr", FilterDISR)
diff --git a/R/FilterGainRatio.R b/R/FilterGainRatio.R
@@ -1,7 +1,7 @@
 #' @title Gain Ratio Filter
 #'
 #' @aliases mlr_filters_gain_ratio
-#' @format [R6::R6Class] inheriting from [Filter].
+#' @format [R6::R6Class] inheriting from [FilterResult].
 #' @include Filter.R
 #'
 #' @description
@@ -15,8 +15,8 @@
 #' task = mlr3::mlr_tasks$get("sonar")
 #' filter = FilterGainRatio$new()
 #' filter$calculate(task)
-#' head(as.data.table(filter), 3)
-FilterGainRatio = R6Class("FilterGainRatio", inherit = Filter,
+#' as.data.table(filter)[1:3]
+FilterGainRatio = R6Class("FilterGainRatio", inherit = FilterResult,
   public = list(
     initialize = function(id = "gain_ratio") {
       super$initialize(
@@ -38,3 +38,5 @@ FilterGainRatio = R6Class("FilterGainRatio", inherit = Filter,
     }
   )
 )
+
+register_filter("gain_ratio", FilterGainRatio)
diff --git a/R/FilterInformationGain.R b/R/FilterInformationGain.R
@@ -1,7 +1,7 @@
 #' @title Information Gain Filter
 #'
 #' @aliases mlr_filters_information_gain
-#' @format [R6::R6Class] inheriting from [Filter].
+#' @format [R6::R6Class] inheriting from [FilterResult].
 #' @include Filter.R
 #'
 #' @description
@@ -15,8 +15,8 @@
 #' task = mlr3::mlr_tasks$get("sonar")
 #' filter = FilterInformationGain$new()
 #' filter$calculate(task)
-#' head(as.data.table(filter), 3)
-FilterInformationGain = R6Class("FilterInformationGain", inherit = Filter,
+#' as.data.table(filter)[1:3]
+FilterInformationGain = R6Class("FilterInformationGain", inherit = FilterResult,
   public = list(
     initialize = function(id = "information_gain") {
       super$initialize(
@@ -37,3 +37,5 @@ FilterInformationGain = R6Class("FilterInformationGain", inherit = Filter,
     }
   )
 )
+
+register_filter("information_gain", FilterInformationGain)
diff --git a/R/FilterJMI.R b/R/FilterJMI.R
@@ -1,7 +1,7 @@
 #' @title Joint Mutual Information Filter
 #'
 #' @aliases mlr_filters_jmi
-#' @format [R6::R6Class] inheriting from [Filter].
+#' @format [R6::R6Class] inheriting from [FilterResult].
 #' @include Filter.R
 #'
 #' @description
@@ -14,8 +14,8 @@
 #' task = mlr3::mlr_tasks$get("iris")
 #' filter = FilterJMI$new()
 #' filter$calculate(task)
-#' head(as.data.table(filter), 3)
-FilterJMI = R6Class("FilterJMI", inherit = Filter,
+#' as.data.table(filter)[1:3]
+FilterJMI = R6Class("FilterJMI", inherit = FilterResult,
   public = list(
     initialize = function(id = "jmi") {
       super$initialize(
@@ -35,3 +35,5 @@ FilterJMI = R6Class("FilterJMI", inherit = Filter,
     }
   )
 )
+
+register_filter("jmi", FilterJMI)
diff --git a/R/FilterJMIM.R b/R/FilterJMIM.R
@@ -1,7 +1,7 @@
 #' @title Minimal Joint Mutual Information Maximisation Filter
 #'
 #' @aliases mlr_filters_jmim
-#' @format [R6::R6Class] inheriting from [Filter].
+#' @format [R6::R6Class] inheriting from [FilterResult].
 #' @include Filter.R
 #'
 #' @description
@@ -14,8 +14,8 @@
 #' task = mlr3::mlr_tasks$get("iris")
 #' filter = FilterJMIM$new()
 #' filter$calculate(task)
-#' head(as.data.table(filter), 3)
-FilterJMIM = R6Class("FilterJMIM", inherit = Filter,
+#' as.data.table(filter)[1:3]
+FilterJMIM = R6Class("FilterJMIM", inherit = FilterResult,
   public = list(
     initialize = function(id = "jmim") {
       super$initialize(

diff --git a/R/FilterKruskalTest.R b/R/FilterKruskalTest.R
@@ -1,7 +1,7 @@
 #' @title Kruskal-Wallis Test Filter
 #'
 #' @aliases mlr_filters_kruskal_test
-#' @format [R6::R6Class] inheriting from [Filter].
+#' @format [R6::R6Class] inheriting from [FilterResult].
 #' @include Filter.R
 #'
 #' @description
@@ -14,8 +14,8 @@
 #' task = mlr3::mlr_tasks$get("iris")
 #' filter = FilterKruskalTest$new()
 #' filter$calculate(task)
-#' head(as.data.table(filter), 3)
-FilterKruskalTest = R6Class("FilterKruskalTest", inherit = Filter,
+#' as.data.table(filter)[1:3]
+FilterKruskalTest = R6Class("FilterKruskalTest", inherit = FilterResult,
   public = list(
     initialize = function(id = "kruskal_test") {
       super$initialize(
@@ -38,3 +38,5 @@ FilterKruskalTest = R6Class("FilterKruskalTest", inherit = Filter,
     }
   )
 )
+
+register_filter("kruskal_test", FilterKruskalTest)
diff --git a/R/FilterLinearCorrelation.R b/R/FilterLinearCorrelation.R
@@ -1,7 +1,7 @@
 #' @title Linear Correlation Filter
 #'
 #' @aliases mlr_filters_linear_correlation
-#' @format [R6::R6Class] inheriting from [Filter].
+#' @format [R6::R6Class] inheriting from [FilterResult].
 #' @include Filter.R
 #'
 #' @description
@@ -14,8 +14,8 @@
 #' task = mlr3::mlr_tasks$get("mtcars")
 #' filter = FilterLinearCorrelation$new()
 #' filter$calculate(task)
-#' head(as.data.table(filter), 3)
-FilterLinearCorrelation = R6Class("FilterLinearCorrelation", inherit = Filter,
+#' as.data.table(filter)[1:3]
+FilterLinearCorrelation = R6Class("FilterLinearCorrelation", inherit = FilterResult,
   public = list(
     initialize = function(id = "linear_correlation") {
       super$initialize(
@@ -37,3 +37,5 @@ FilterLinearCorrelation = R6Class("FilterLinearCorrelation", inherit = Filter,
     }
   )
 )
+
+register_filter("linear_correlation", FilterLinearCorrelation)
diff --git a/R/FilterMIM.R b/R/FilterMIM.R
@@ -1,7 +1,7 @@
 #' @title Conditional Mutual Information Based Feature Selection Filter
 #'
 #' @aliases mlr_filters_mim
-#' @format [R6::R6Class] inheriting from [Filter].
+#' @format [R6::R6Class] inheriting from [FilterResult].
 #' @include Filter.R
 #'
 #' @description
@@ -14,8 +14,8 @@
 #' task = mlr3::mlr_tasks$get("iris")
 #' filter = FilterMIM$new()
 #' filter$calculate(task)
-#' head(as.data.table(filter), 3)
-FilterMIM = R6Class("FilterMIM", inherit = Filter,
+#' as.data.table(filter)[1:3]
+FilterMIM = R6Class("FilterMIM", inherit = FilterResult,
   public = list(
     initialize = function(id = "mim") {
       super$initialize(
@@ -35,3 +35,5 @@ FilterMIM = R6Class("FilterMIM", inherit = Filter,
     }
   )
 )
+
+register_filter("mim", FilterMIM)
diff --git a/R/FilterMRMR.R b/R/FilterMRMR.R
@@ -1,7 +1,7 @@
 #' @title Minimum redundancy maximal relevancy filter
 #'
 #' @aliases mlr_filters_MRMR
-#' @format [R6::R6Class] inheriting from [Filter].
+#' @format [R6::R6Class] inheriting from [FilterResult].
 #' @include Filter.R
 #'
 #' @description
@@ -15,7 +15,7 @@
 #' filter = FilterMRMR$new()
 #' filter$calculate(task)
 #' head(as.data.table(filter), 3)
-FilterMRMR = R6Class("FilterMRMR", inherit = Filter,
+FilterMRMR = R6Class("FilterMRMR", inherit = FilterResult,
   public = list(
     initialize = function(id = "MRMR") {
       super$initialize(

diff --git a/R/FilterNJMIM.R b/R/FilterNJMIM.R
@@ -1,7 +1,7 @@
 #' @title Minimal Normalised Joint Mutual Information Maximisation Filter
 #'
 #' @aliases mlr_filters_njmim
-#' @format [R6::R6Class] inheriting from [Filter].
+#' @format [R6::R6Class] inheriting from [FilterResult].
 #' @include Filter.R
 #'
 #' @description
@@ -14,8 +14,8 @@
 #' task = mlr3::mlr_tasks$get("iris")
 #' filter = FilterNJMIM$new()
 #' filter$calculate(task)
-#' head(as.data.table(filter), 3)
-FilterNJMIM = R6Class("FilterNJMIM", inherit = Filter,
+#' as.data.table(filter)[1:3]
+FilterNJMIM = R6Class("FilterNJMIM", inherit = FilterResult,
   public = list(
     initialize = function(id = "njmim") {
       super$initialize(
@@ -35,3 +35,5 @@ FilterNJMIM = R6Class("FilterNJMIM", inherit = Filter,
     }
   )
 )
+
+register_filter("njmim", FilterNJMIM)
diff --git a/R/FilterRankCorrelation.R b/R/FilterRankCorrelation.R
@@ -1,7 +1,7 @@
 #' @title Rank Correlation Filter
 #'
 #' @aliases mlr_filters_rank_correlation
-#' @format [R6::R6Class] inheriting from [Filter].
+#' @format [R6::R6Class] inheriting from [FilterResult].
 #' @include Filter.R
 #'
 #' @description
@@ -14,8 +14,8 @@
 #' task = mlr3::mlr_tasks$get("mtcars")
 #' filter = FilterRankCorrelation$new()
 #' filter$calculate(task)
-#' head(as.data.table(filter), 3)
-FilterRankCorrelation = R6Class("FilterRankCorrelation", inherit = Filter,
+#' as.data.table(filter)[1:3]
+FilterRankCorrelation = R6Class("FilterRankCorrelation", inherit = FilterResult,
   public = list(
     initialize = function(id = "rank_correlation") {
       super$initialize(
@@ -37,3 +37,5 @@ FilterRankCorrelation = R6Class("FilterRankCorrelation", inherit = Filter,
     }
   )
 )
+
+register_filter("rank_correlation", FilterRankCorrelation)